Incredible but true - molecules can now do sums, according to UK
chemists. New research means we are a step closer to building a supercomputer
that is no bigger than a pinhead.

by David Bradley

Prasanna 'AP' de Silva and Nathan McClenaghan at Queen's University,
Belfast have used molecules that switch on and off depending on
a chemical signal, and can produce a tiny burst of light representing
a binary number 1. Such molecules can work as the equivalent of
the tiny logic gates on a silicon chip, making decisions on each
bit of computer information that passes through them. By running
them together the researchers can carry out arithmetic operations.

Normally, a vast array of millions of transistors etched on to
a silicon chip is at the heart of a computer, but chips are like
whole cities on the molecular scale and when real estate is getting
tighter and tighter it is time for the molecular architects to step
in.

'The extension of information processing and computation to the
molecular level will only be possible when molecular logic gates
are available,' according to Vincenzo Balzani of Bologna University.
He believes chemists can design and construct molecules to do the
work of silicon chips but in a much smaller space and far faster.

There are several different logic gates used in computing. For
instance, an 'AND' gate gives an 'on' or '1' output when both its
inputs are '1'. An 'OR' gate, is only 'on' or '1' when its inputs
are '1' or '0'. The slightly bizarre 'XOR' (eXclusive OR) gate acts
like a 'spot the difference' unit giving no output if both inputs
are 1s or 0s but a '1' if they are '1 and 0' or '0 and 1'. The NOT,
OR, INH, and NOR gates and many others all work together to do addition,
subtraction, multiplication, and division. With those mathematical
functions, you can carry out any conceivable computer process -
from displaying a single word on-screen to rendering a multimedia
web site. Computation always reduces to maths.

PhotosToGo

All
computation is based on simple logic gates

De Silva and his colleagues previously built molecular versions
of several logic gates, including the AND and XOR. The gates are
based on tiny claw- shaped molecules that trap different ions. They
then use these ions to represent binary 1's. When two different
ions are present (a calcium and a hydrogen) the claw molecule glows
blue, representing a '1' output. With no ions present the molecule
stays switched off, there is no glow, so the output is 0. The XOR
molecule works similarly but lights up only when the two inputs
are different.

The clever bit, explains de Silva, comes when you makes these two
logic gates work together. Say you're adding two numbers (in binary)
- 1 and 1. When the ions representing these numbers are present
and are trapped by the AND gate it lights up - the output is a 1.
You can call this the 'carry over' number of primary school sums.
The XOR with the same combination of ions does not illuminate it
gives a 0. So, 1 add 1 equals zero, carry one, which in binary is
'1-0'. In other words 1+1=2.

PhotosToGo

DNA
is one of the most efficient digital systems known

'Such logic operations are the basis of all computing,' explains
de Silva, ' by using molecules instead of silicon chips we hope
to be able to perform small-scale computational operations in very
small spaces'. Scientists are on the verge of being able to manipulate
and observe single molecules using fluorescent sensors, and will
soon be able to 'see' the glow from individual logic gates. De Silva
adds that, 'The first "real" device applications are expected
to occur fastest in the fields of biotechnology and combinatorial
chemistry where small volumes are common.'

Nature, though, may have provided scientists with an alternative
to building logic gates, at least for some kinds of 'number crunching'
computational problems.

The genetic code formed from the nucleic acids, RNA and DNA, is
one of the neatest digital information systems we know. In the early
1990s, Leonard Adleman at the University of Southern California
began figuring out how this digital code might be used to solve
mathematical puzzles, such as the travelling-salesman problem. Adleman
used different strands of DNA to represent different routes a salesman
might take between a group of towns so that his total journey time
is kept to a minimum.

A set of enzymes that can single out those sequences corresponding
to a shorter journey were then used to split, or cleave, the DNA
strands that are not optimum, step by step. Eventually, the array
of combinations is reduced to a single strand representing the best
route.

PhotosToGo

How
many ways can two opposing knights be placed on a chessboard
so they are not attacking each other?
Could the answer be found with an RNA calculator?

Earlier this year, two other research groups have applied similar
thinking to a second puzzle that asks the question, 'How many ways
can two opposing knights be placed on a chessboard so they are not
attacking each other?'

Laura Landweber collaborated with Richard Lipton, Dirk Faulhammer
and Anthony Cukras to see whether they could solve this chess problem
using DNA's chemical cousin ribonucleic acid (RNA). To make the
experiment simpler they reduced the chessboard to a 3x3 grid and
used different strands of RNA to form combinations each representing
a location of the two knights on the board.

An enzyme - ribonuclease - was then used to seek out specific combinations
of bases along the strands of RNA and cleaving those that do not
match the correct answers to the problem. They came up with most
of the answers in a very short time but the fact that it works alone
demonstrates the potential of an RNA calculator.

Meanwhile, Lloyd Smith and his colleagues at the University of
Wisconsin- Madison demonstrated a slightly different approach to
the same puzzle using DNA itself. However, their system is built
on a solid support, which lends itself better than dissolved molecules,
to more direct connection to external devices, such as electronic
components.

Of course Science Fiction writers got there first, the computer
system of the latest Star Trek ship (Voyager) is biological - only
a molecular system is small and powerful enough to run a ship of
that complexity!

With logic gates adding up and strands of DNA solving age-old maths
puzzles, it is perhaps only a few more years before chemistry will
come up with a prescription for a molecular computer.Thorri Gunnlaugsson
a former member of de Silva's research team and now heading his
own group at Trinity College Dublin asks us to imagine a memory
chip the size of a sugar cube carrying as much information as a
thousand billion CD-ROMs or a molecular chip running a thousand
times faster than the PC on your desktop. Sadly, there might then
come a time when a computer crash doesn't just leave you frustrated
by a blank screen but might soak your desktop too!